BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779290.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 15,373,412 number of mapped reads = 14,952,407 (97.26%) number of supplementary alignments = 36,551 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,533,746 number of mapped paired reads (second in pair) = 7,418,661 number of mapped paired reads (both in pair) = 14,819,390 number of mapped paired reads (singletons) = 133,017 number of mapped bases = 1,190,322,027 bp number of sequenced bases = 1,190,110,829 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 269,481 duplication rate = 1.7% >>>>>>> Insert size mean insert size = 41,740.1135 std insert size = 1,929,229.1892 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 53.0167 >>>>>>> ACTG content number of A's = 364,401,376 bp (30.62%) number of C's = 229,232,672 bp (19.26%) number of T's = 363,330,927 bp (30.53%) number of G's = 232,921,847 bp (19.57%) number of N's = 224,007 bp (0.02%) GC percentage = 38.83% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 4,465,282 number of insertions = 82,456 mapped reads with insertion percentage = 0.55% number of deletions = 102,473 mapped reads with deletion percentage = 0.68% homopolymer indels = 46.99% >>>>>>> Coverage mean coverageData = 0.3845X std coverageData = 1.1367X There is a 20.09% of reference with a coverageData >= 1X There is a 8.48% of reference with a coverageData >= 2X There is a 4.07% of reference with a coverageData >= 3X There is a 2.16% of reference with a coverageData >= 4X There is a 1.23% of reference with a coverageData >= 5X There is a 0.74% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 112537371 0.45150287108010856 1.301607295809102 chr2 243199373 76891453 0.3161663290965804 0.9249486075339576 chr3 198022430 87089073 0.4397939819241689 1.088807238389084 chr4 191154276 96057169 0.5025112229244613 1.172314284015588 chr5 180915260 86505028 0.4781521912524129 1.164574540698182 chr6 171115067 68126564 0.3981330527720274 1.029272772604046 chr7 159138663 110333765 0.693318411252456 2.1094937817170174 chr8 146364022 82141564 0.5612141759810345 1.2806680062445248 chr9 141213431 41257292 0.2921626626294492 0.8703310363836284 chr10 135534747 25207016 0.18598194601713464 1.0947509493456042 chr11 135006516 54326607 0.4023998886098209 1.115993409892233 chr12 133851895 59818641 0.44690171177628824 1.171796117988643 chr13 115169878 33556406 0.2913644312447739 0.8357592884328624 chr14 107349540 37977423 0.3537735047583809 0.9550727133789635 chr15 102531392 24321519 0.2372104633086421 0.8554911094947455 chr16 90354753 15226247 0.168516281595059 0.6403080816976696 chr17 81195210 19144578 0.2357845739914953 0.7556396643119074 chr18 78077248 22063813 0.2825895323564683 0.8234138659401098 chr19 59128983 13253097 0.22413876118924622 0.8059043355138427 chr20 63025520 23987697 0.38060292084857056 1.0441886525119697 chr21 48129895 8727853 0.18133953959384286 0.6514046137480578 chr22 51304566 5346402 0.10420908735491496 0.44758901626630226 chrMT 16571 1016 0.061311930480960716 0.31886264659438424 chrX 155270560 85564036 0.551064129607055 1.348370544713977 chrY 59373566 860397 0.01449124682859709 0.1913342976333482